glow_bonemed EDA
Derek Rogers,
2023-04-04
library(aplore3)## Warning: package 'aplore3' was built under R version 4.2.3library(ggplot2)
library(plotly)##
## Attaching package: 'plotly'## The following object is masked from 'package:ggplot2':
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## last_plot## The following object is masked from 'package:stats':
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## filter## The following object is masked from 'package:graphics':
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## layoutData Format: A data.frame with 500 rows and 18 variables such as:
priorfrac - If the patient previously had a fracture age weight height bmi premeno momfrac armassist smoke raterisk fracscore fracture bonemed - Bone medications at enrollment (1: No, 2: Yes) bonemed_fu - Bone medications at follow-up (1: No, 2: Yes) bonetreat - Bone medications both at enrollment and follow-up (1: No, 2: Yes)
head(glow_bonemed)## sub_id site_id phy_id priorfrac age weight height bmi premeno momfrac
## 1 1 1 14 No 62 70.3 158 28.16055 No No
## 2 2 4 284 No 65 87.1 160 34.02344 No No
## 3 3 6 305 Yes 88 50.8 157 20.60936 No Yes
## 4 4 6 309 No 82 62.1 160 24.25781 No No
## 5 5 1 37 No 61 68.0 152 29.43213 No No
## 6 6 5 299 Yes 67 68.0 161 26.23356 No No
## armassist smoke raterisk fracscore fracture bonemed bonemed_fu bonetreat
## 1 No No Same 1 No No No No
## 2 No No Same 2 No No No No
## 3 Yes No Less 11 No No No No
## 4 No No Less 5 No No No No
## 5 No No Same 1 No No No No
## 6 No Yes Same 4 No No No Nosummary(glow_bonemed)## sub_id site_id phy_id priorfrac age
## Min. : 1.0 Min. :1.000 Min. : 1.00 No :374 Min. :55.00
## 1st Qu.:125.8 1st Qu.:2.000 1st Qu.: 57.75 Yes:126 1st Qu.:61.00
## Median :250.5 Median :3.000 Median :182.50 Median :67.00
## Mean :250.5 Mean :3.436 Mean :178.55 Mean :68.56
## 3rd Qu.:375.2 3rd Qu.:5.000 3rd Qu.:298.00 3rd Qu.:76.00
## Max. :500.0 Max. :6.000 Max. :325.00 Max. :90.00
## weight height bmi premeno momfrac armassist
## Min. : 39.90 Min. :134.0 Min. :14.88 No :403 No :435 No :312
## 1st Qu.: 59.90 1st Qu.:157.0 1st Qu.:23.27 Yes: 97 Yes: 65 Yes:188
## Median : 68.00 Median :161.5 Median :26.42
## Mean : 71.82 Mean :161.4 Mean :27.55
## 3rd Qu.: 81.30 3rd Qu.:165.0 3rd Qu.:30.79
## Max. :127.00 Max. :199.0 Max. :49.08
## smoke raterisk fracscore fracture bonemed bonemed_fu
## No :465 Less :167 Min. : 0.000 No :375 No :371 No :361
## Yes: 35 Same :186 1st Qu.: 2.000 Yes:125 Yes:129 Yes:139
## Greater:147 Median : 3.000
## Mean : 3.698
## 3rd Qu.: 5.000
## Max. :11.000
## bonetreat
## No :382
## Yes:118
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## From the age vs bmi and fracscore vs age scatter plots there doesn’t seem to be any groupings or separations between fracture yes/no categorical response.
As age increases the average bmi decreases There is a strong positive correlation between age and fracscore
plot(glow_bonemed[, c(5:8, 14)])
ggplot(glow_bonemed, aes(x = age, y = bmi, color = fracture)) +
geom_jitter()
ggplot(glow_bonemed, aes(x = fracscore, y = age, color = fracture)) +
geom_jitter()
ggplot(glow_bonemed, aes(x = weight, y = height, color = fracture)) +
geom_jitter()
fracture3dplot = plot_ly(glow_bonemed,
x = ~age,
y = ~height,
z = ~bmi,
color = ~fracture,
colors = c('#0C4B8E', '#BF382A')) %>% add_markers()
fracture3dplotClustering EDA
library(RColorBrewer)
library(pheatmap)## Warning: package 'pheatmap' was built under R version 4.2.3library(cluster)pheatmap(glow_bonemed[, c(5,8)], scale = "column", fontsize_row = 0.1, cluster_cols = F, legend = T, color = colorRampPalette(c("blue", "white", "red"), space = "rgb")(100))
pheatmap(glow_bonemed[, 5:8], scale = "column", fontsize_row = 0.1, cluster_cols = F, legend = T, color = colorRampPalette(c("blue", "white", "red"), space = "rgb")(100))
zScoreScale = scale(glow_bonemed[, 5:8])
zScoreDistance = dist(zScoreScale)
continuousVariableClustering = hclust(zScoreDistance, method = "complete")
plot(continuousVariableClustering)
Sources: Hosmer, D.W., Lemeshow, S. and Sturdivant, R.X. (2013) Applied Logistic Regression, 3rd ed., New York: Wiley
https://cran.r-project.org/web/packages/aplore3/aplore3.pdf#page=11&zoom=100,132,90